Structure Gromos

Standard molecular mechanics (MM) methods (e.g. the popular force fields developed for AMBER, CHARMM and GROMOS decribed in Section 2 above) provide a good description of protein structure and dynamics, but cannot be used to model chemical reactions. This limitation is due their simple functional forms (e.g. harmonic terms for bond stretching) and inability to model changes in electronic polarization (because of the invariant point partial atomic charge used by these molecular mechanics methods to represent electrostatic interactions). 

The first important dynamic CyD studies published in 1987 and 1988 were the result of cooperation by the theoreticians van Gunsteren and Koehler with the X-ray specialist Saenger [98, 99, 100, 101, 102]. The aim of these studies was twofold on the one hand, they served the development of the GROMOS force field [103] while on the other they had to show that DSs for such complicated systems as CyDs were feasible. Starting from the experimental structures, these simulations of 15 or 20 ps, very short by today s standards, are of historical interest only. Similarly, the work by Mark et al. [104] of 1994 on free perturbation calculations was mainly devoted to the development of the method. 

Figure 16.1. Molecular structure of some amphiphilic solutes, (a) Dimethyl sulphoxide (DMSO), (b) methanol (MeOH), (c) ethanol (EtOH), (d) tert-butyl alcohol (TEA), (e) acetone. For all these solutes the partial charges are indicated on the corresponding atoms according to the GROMOS-96 force field, (f) Molecular structure of 1,4-dioxane. For 1,4-dioxane the partial charges are indicated on the respective atoms according to / Am. Chem. Soc., 127 (2005), 11019-11028.

The structure, conformation and intramolecular hydrogen bonds of crystalline and aqueous sucrose have been discussed in detail. Evidence for a transient inter-residue hydrogen bond in aqueous sucrose (0-2- -H O-T) has been discovered by ROESY spectroscopy imder supercooled conditions.Combined use of high resolution NMR techniques and dynamics simulations furnished a new model for the dynamical conformational behaviour of sucrose in water in which internal motions occur at the same rate as overall tumbling. A GROMOS force field analysis, modified to include a potential energy term for the fxo-anomeric effect, has been assessed for efficiency by application to a conformational analysis of a-maltose. ... 

Molecular modeling and computer simulation with empirical potential energy function (force field) are now routinely carried out to help understand and predict structures and dynamics of proteins and other macromolecules of biological relevance in water and membrane environments. After over 40 years of development, popular force fields such as AMBER, CHARMM, OPLS and GROMOS have been widely employed in biomolecular simulations. These force fields are used dominantly in highly optimized molecular dynamics... 

Figure 2 ANOLEA and GROMOS analysis of the California Quail Lysozyme C (P00699) protein model constructed by SWISS-MODEL/ For both analysis methods, negative values are preferred and indicate structurally sound models.

The relevant literature on lactose dissolution in water has been reviewed in a paper which describes a mathematical model for this process/ Short time scale molecular dynamics simulations of sucrose in water and DMSO indicated that the conformations in both solvents are similar to that accepted in the crystalline state/ Solid-liquid equilibria for aqueous sucrose have been studied by use of an UNIQUAC model/ A comparison of GROMOS force field and Ha force field in molecular dynamics simulations of glucose crystals indicated superior performance by the latter method/ Predicted crystal structures of P-D-glucose, P-D-galactose, P-D-allose, a-D-glucose, a-D-galactose, and a-D-talose matched or nearly matched the X-ray-derived data in four cases/ ... 

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